ct.PantherPathwayEnrichment: Run a (limited) Pathway Enrichment Analysis on the results of...

Run a (limited) Pathway Enrichment Analysis on the results of a Crispr experiment.

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Description

This function enables some limited geneset enrichment-type analysis of data derived from a pooled Crispr
screen using the PANTHER pathway database. Specifically, it identifies the set of targets significantly enriched or
depleted in a summaryDF object returned from ct.generateResults and compares that set to the remaining
targets in the screening library using a hypergeometric test.

Note that many Crispr gRNA libraries specifically target biased sets of genes, often focusing on genes involved
in a particular pathway or encoding proteins with a shared biological property. Consequently, the enrichment results
returned by this function represent the pathways containing genes disproportionately targeted *within the context
of the screen*, and may or may not be informative of the underlying biology in question. This means that
pathways not targeted by a Crispr library will obviously never be enriched within the positive target set regardless of
their biological relevance, and pathways enriched within a focused library screen are similarly expected to partially
reflect the composition of the library and other confounding issues (e.g., number of targets within a pathway).
Analysts should therefore use this function with care. For example, it might be unsurprising to detect pathways related
to histone modification within a screen employing a crispr library targeting epigenetic regulators.